1. Field of the Invention
The present invention relates to the field of molecular biology and provides improved methods for the replication and amplification of ribonucleic acid (RNA) sequences. In a preferred embodiment, the invention provides a method for synthesizing a complementary DNA copy from an RNA template with a thermoactive DNA polymerase. In another aspect,the invention provides methods for amplifying a DNA segment for an RNA template using a thermostable DNA polymerase.
2. Description of the Related Art
The term "reverse transcriptase" describes a class of polymerases characterized as RNA-dependent DNA polymerases. All known reverse transcriptases require a primer to synthesize a DNA transcript from an RNA template. Historically, reverse transcriptase has been used primarily to transcribe mRNA into cDNA which can then be cloned into a vector for further manipulation.
Avian myoblastosis virus (AMV) reverse transcriptase was the first widely used RNA-dependent DNA polymerase (Verma, 1977, Biochem. Biophys. Acta 473:1). The enzyme has both a 5'-3'RNA-directed DNA polymerase activity as well as an RNaseH activity. RNaseH is a processive 5' and 3' ribonuclease specific for the RNA strand of RNA-DNA hybrids (Perbal, 1984, A Practical Guide to Molecular Cloning, Wiley & Sons New York). Errors in transcription cannot be corrected by reverse transcriptase because known viral reverse transcriptases lack the 3'AE5' exonuclease acitivity necessary for proofreading (Saunders and Saunders, 1987, Microbial Genetics Applied to Biotechnology, Croom Helm, London). A detailed study of the activity of AMV reverse transcriptase and its associated RNaseH activity has been presented by Berger et al., 1983, Biochemistry 22:2365-2372.
Berger et al. found that the rate limiting step in RNA transcription was initiation of the transcription reaction, rather than the sequential polymerization of additional nucleotides. To overcome this limitation, use of a stoichiometric, rather than catalytic, quantity of reverse transcriptase is frequently recommended (Buell et al., 1978, J. Biol. Chem. 253:2471-2482; Wickens et al., 1978, J. Bio. Chem. 253:2483-2495; Yoo et al., 1982, Proc. Nat. Acad. Sci. USA 80:1194-1198; and Okayama and Berg, 1982, Mol. Cell. Biol. 2:161-170). However, when stoichiometric amounts of reverse transcriptase are used, the low level of RNaseH activity is significant and may be responsible for fragmented cDNAs and limited cDNA yields. Christopher et al., 1980, Eur. J. Biochem. 111:4190-4231, and Michelson et al., 1983, Proc. Nat. Acad. Sci. USA 80:472-476, have suggested that including an RNase inhibitor in cDNA reactions could alleviate this problem.
DNA polymerases isolated from mesophilic microorganisms such as E. coli. have been extensively researched (see, for example, Bessman et al., 1957, J. Biol. Chem. 233:171-177 and Buttin and Kornberg, 1966, J. Bio. Chem. 241:5419-5427). E. coli DNA polymerase I (Pol I) is useful for a number of applications including: nick-translation reactions, DNA sequencing, in vitro mutagenesis, second strand cDNA synthesis, polymerase chain reaction (PCR), and blunt end formation for linker ligation (Maniatis et al., 1982, Molecular Cloning: A Laboratory Manual Cold Spring Harbor, N.Y.).
Several laboratories have shown that some DNA polymerases are capable of in vitro reverse transcription of RNA (Karkas, 1973, Proc. Nat. Acad. Sci. USA 70:3834-3838; Gulati et al., 1974, Proc. Nat. Acad. Sci. USA 71:1035-1039; and Wittig and Wittig, 1978, Nuc. Acid Res. 5:1165-1178). Gulati et al. found that E. coli Pol I could be used to transcribe Qb viral RNA using oligo(dT).sub.10 as a primer. Wittig and Wittig have shown that E. coli Pol I can be used to reverse transcribe tRNA that has been enzymatically elongated with oligo(dA). However, as Gulati et al. demonstrated, the amount of enzyme required and the small size of the cDNA product suggests that the reverse transcriptase activity of E. coli Pol I has little practical value.
The use of thermostable enzymes to amplify existing nucleic acid sequences in amounts that are large compared to the amount initially present was described in U.S. Pat. Nos. 4,683,195 and 4,683,202, which describe the polymerase chain reaction (PCR) processes. These patents are incorporated herein by reference. Primers, template, nucleoside triphosphates, the appropriate buffer and reaction conditions, and a polymerase are used in the PCR process, which involves denaturation of target DNA, hybridization of primers, and synthesis of complementary strands. The extension product of each primer becomes a template for the production of the desired nucleic acid sequence. These patents disclose that, if the polymerase employed is a thermostable enzyme, then polymerase need not be added after every denaturation step, because heat will not destroy the polymerase activity.
Thermostable DNA polymerases are not permanently inactivated even when heated to 93.degree.-95.degree. C. for brief periods of time, as, for example, in the practice of DNA amplification by PCR. In contrast, at this elevated temperature E. coli DNA Pol I and previously described reverse transcriptases are inactivated.
The thermostable DNA polymerase from Thermus aquaticus (Taq) has been cloned, expressed, and purified from recombinant cells as described in Lawyer et al., 1989, J. Biol. Chem. 264:6427-6437, and U.S. Pat. Nos. 4,889,818 and 5,079,352, which are incorporated herein by reference. Crude preparations of a DNA polymerase activity isolated from T. aquaticus have been described by others (Chien et al., 1976, J. Bacteriol. 127:1550-1557, and Kaledin et al., 1980, Biokymiya 45:644-651).
The thermostable DNA polymerase from Thermus thermophilus (Tth) has also been purified and is described in PCT No. WO 91/09950, published Jul. 11, 1991, which is incorporated herein by reference. The '967 patent application also describes that the gene encoding Tth DNA polymerase enzyme from Thermus thermophilus has been identified and cloned. Recombinant Tth provides an alternative means for preparing the thermostable enzyme. The thermostable DNA polymerase from Thermotoga maritima has been identified and cloned and is described in copending attorney docket No. 2570, filed Aug. 13, 1990, and incorporated herein by reference.
PCR requires a nucleic acid template and appropriate primers for amplification. The DNA to be amplified may be synthetic or genomic, contained in a plasmid, or contained in a heterogenous sample. If the nucleotide sequence to be amplified is RNA, the nucleic acid molecule is first treated with reverse transcriptase in the presence of a primer to provide a cDNA template for amplification. Prior to the present invention, amplification of RNA necessitated a reverse transcription step with, e.g., a non-thermostable reverse transcriptase such as Molony Murine Leukemia Virus Reverse Transcriptase (MoMuLV RT) or AMV-RT, followed by treatment of the resulting single-stranded cDNA with a DNA polymerase. The amplification of RNA could be gently simplified by the availability of a method for reverse transcribing RNA and amplifying DNA with a single enzyme.
The present invention addresses this need and provides high temperature cDNA synthesis by thermoactive DNA polymerases. The invention also provides methods for the efficient amplification of RNA sequences requiring only one enzyme, a thermostable DNA polymerase. These methods offer simplicity and enhanced specificity over currently known methods.